[2024-01-24 15:26:39,835] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:39,839] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:39,839] [INFO] DQC Reference Directory: /var/lib/cwl/stg1113d3f0-afcb-4585-8904-00f26cda6d5e/dqc_reference
[2024-01-24 15:26:41,200] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:41,201] [INFO] Task started: Prodigal
[2024-01-24 15:26:41,201] [INFO] Running command: gunzip -c /var/lib/cwl/stg48bd5268-e574-4436-9d09-3e15564d465e/GCF_004295345.1_ASM429534v1_genomic.fna.gz | prodigal -d GCF_004295345.1_ASM429534v1_genomic.fna/cds.fna -a GCF_004295345.1_ASM429534v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:53,115] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:53,116] [INFO] Task started: HMMsearch
[2024-01-24 15:26:53,116] [INFO] Running command: hmmsearch --tblout GCF_004295345.1_ASM429534v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1113d3f0-afcb-4585-8904-00f26cda6d5e/dqc_reference/reference_markers.hmm GCF_004295345.1_ASM429534v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:53,433] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:53,435] [INFO] Found 6/6 markers.
[2024-01-24 15:26:53,478] [INFO] Query marker FASTA was written to GCF_004295345.1_ASM429534v1_genomic.fna/markers.fasta
[2024-01-24 15:26:53,479] [INFO] Task started: Blastn
[2024-01-24 15:26:53,479] [INFO] Running command: blastn -query GCF_004295345.1_ASM429534v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1113d3f0-afcb-4585-8904-00f26cda6d5e/dqc_reference/reference_markers.fasta -out GCF_004295345.1_ASM429534v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:54,333] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:54,337] [INFO] Selected 20 target genomes.
[2024-01-24 15:26:54,337] [INFO] Target genome list was writen to GCF_004295345.1_ASM429534v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:54,346] [INFO] Task started: fastANI
[2024-01-24 15:26:54,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg48bd5268-e574-4436-9d09-3e15564d465e/GCF_004295345.1_ASM429534v1_genomic.fna.gz --refList GCF_004295345.1_ASM429534v1_genomic.fna/target_genomes.txt --output GCF_004295345.1_ASM429534v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:12,076] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:12,077] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1113d3f0-afcb-4585-8904-00f26cda6d5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:12,077] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1113d3f0-afcb-4585-8904-00f26cda6d5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:12,092] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:12,093] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:12,093] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Shewanella maritima	strain=D4-2	GCA_004295345.1	2520507	2520507	type	True	100.0	1568	1572	95	conclusive
Shewanella intestini	strain=MCCC 1A01895	GCA_018221465.1	2017544	2017544	type	True	78.9751	442	1572	95	below_threshold
Shewanella japonica	strain=KCTC 22435	GCA_002075795.1	93973	93973	type	True	78.9539	353	1572	95	below_threshold
Shewanella pealeana	strain=ATCC 700345	GCA_000018285.1	70864	70864	type	True	78.9503	275	1572	95	below_threshold
Shewanella vesiculosa	strain=M7	GCA_021560015.1	518738	518738	type	True	78.7248	309	1572	95	below_threshold
Shewanella psychromarinicola	strain=M2	GCA_003855155.1	2487742	2487742	type	True	78.701	291	1572	95	below_threshold
Shewanella olleyana	strain=LMG 21437	GCA_023283825.1	135626	135626	type	True	78.6168	344	1572	95	below_threshold
Shewanella electrodiphila	strain=DSM 24955	GCA_023283985.1	934143	934143	type	True	78.4854	342	1572	95	below_threshold
Shewanella litoralis	strain=JCM 32306	GCA_009828585.1	2282700	2282700	type	True	78.3478	341	1572	95	below_threshold
Shewanella sairae	strain=LMG 21408	GCA_023283535.1	190310	190310	type	True	78.2919	250	1572	95	below_threshold
Shewanella saliphila	strain=JCM 32304	GCA_014648295.1	2282698	2282698	type	True	78.2891	350	1572	95	below_threshold
Shewanella oncorhynchi	strain=S-1	GCA_012584455.1	2726434	2726434	type	True	78.272	221	1572	95	below_threshold
Shewanella saliphila	strain=KCTC 62131	GCA_023283695.1	2282698	2282698	type	True	78.2579	351	1572	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	78.2054	321	1572	95	below_threshold
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	78.1993	312	1572	95	below_threshold
Shewanella inventionis	strain=CGMCC 1.15339	GCA_014641855.1	1738770	1738770	type	True	78.199	330	1572	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	78.1942	332	1572	95	below_threshold
Shewanella aestuarii	strain=JCM 17801	GCA_023283685.1	1028752	1028752	type	True	78.1374	318	1572	95	below_threshold
Shewanella schlegeliana	strain=LMG 21406	GCA_023283605.1	190308	190308	type	True	78.1363	236	1572	95	below_threshold
Shewanella ulleungensis	strain=JCM 32305	GCA_014648315.1	2282699	2282699	type	True	78.0867	340	1572	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:12,095] [INFO] DFAST Taxonomy check result was written to GCF_004295345.1_ASM429534v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:12,095] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:12,095] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:12,096] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1113d3f0-afcb-4585-8904-00f26cda6d5e/dqc_reference/checkm_data
[2024-01-24 15:27:12,096] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:12,144] [INFO] Task started: CheckM
[2024-01-24 15:27:12,144] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004295345.1_ASM429534v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004295345.1_ASM429534v1_genomic.fna/checkm_input GCF_004295345.1_ASM429534v1_genomic.fna/checkm_result
[2024-01-24 15:27:52,856] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:52,857] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:52,879] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:52,879] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:52,879] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004295345.1_ASM429534v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:52,880] [INFO] Task started: Blastn
[2024-01-24 15:27:52,880] [INFO] Running command: blastn -query GCF_004295345.1_ASM429534v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1113d3f0-afcb-4585-8904-00f26cda6d5e/dqc_reference/reference_markers_gtdb.fasta -out GCF_004295345.1_ASM429534v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:54,158] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:54,162] [INFO] Selected 17 target genomes.
[2024-01-24 15:27:54,162] [INFO] Target genome list was writen to GCF_004295345.1_ASM429534v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:54,176] [INFO] Task started: fastANI
[2024-01-24 15:27:54,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg48bd5268-e574-4436-9d09-3e15564d465e/GCF_004295345.1_ASM429534v1_genomic.fna.gz --refList GCF_004295345.1_ASM429534v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004295345.1_ASM429534v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:09,536] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:09,561] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:09,562] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_004295345.1	s__Shewanella maritima	100.0	1568	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.24	98.24	0.95	0.95	2	conclusive
GCF_002966515.1	s__Shewanella sp002966515	79.2805	231	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.53	97.30	0.89	0.86	10	-
GCF_002075795.1	s__Shewanella japonica	79.01	354	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.37	97.91	0.95	0.93	6	-
GCF_000018285.1	s__Shewanella pealeana	78.9908	275	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018221465.1	s__Shewanella intestini	78.976	442	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_011765625.1	s__Shewanella aestuarii_A	78.9086	337	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003855395.1	s__Shewanella livingstonensis	78.7542	298	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797885.1	s__Shewanella vesiculosa	78.662	306	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.53	98.48	0.92	0.86	17	-
GCF_003855155.1	s__Shewanella sp002836275	78.5058	287	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.14	98.29	0.96	0.92	3	-
GCF_002873615.1	s__Shewanella sp002873615	78.3774	341	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828585.1	s__Shewanella litoralis	78.3566	340	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014163735.1	s__Shewanella sp014163735	78.3332	233	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009663145.1	s__Shewanella sp009663145	78.3084	358	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648295.1	s__Shewanella saliphila	78.2813	352	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_014641855.1	s__Shewanella inventionis	78.2024	329	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648315.1	s__Shewanella ulleungensis	78.0682	340	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518605.1	s__Shewanella fidelis	77.8632	283	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.11	97.11	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:09,563] [INFO] GTDB search result was written to GCF_004295345.1_ASM429534v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:09,564] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:09,570] [INFO] DFAST_QC result json was written to GCF_004295345.1_ASM429534v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:09,570] [INFO] DFAST_QC completed!
[2024-01-24 15:28:09,570] [INFO] Total running time: 0h1m30s